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Related Experiment Video

Updated: Dec 15, 2025

Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation

Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation

Published on: November 26, 2018

AncesTree: An interactive immunoglobulin lineage tree visualizer.

Mathilde Foglierini^1,2, Leontios Pappas¹, Antonio Lanzavecchia¹

¹Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland.

Plos Computational Biology

|July 11, 2020

Summary

This summary is machine-generated.

Researchers can now explore antibody clonal evolution and somatic mutations with AncesTree, a new graphical tool. This software aids in understanding antibody affinity maturation and reconstructing lineage evolution from sequencing data.

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

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Immunoglobulin Gene Sequence Analysis In Chronic Lymphocytic Leukemia: From Patient Material To Sequence Interpretation

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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Published on: December 28, 2015

Area of Science:

Immunology
Bioinformatics
Computational Biology

Background:

High-throughput sequencing of immunoglobulin genes enables antibody repertoire analysis and clonal lineage evolution studies.
Understanding antibody affinity maturation is crucial for developing high-affinity or broadly neutralizing antibodies.
Phylogenetic analysis helps identify key somatic mutations for optimal antigen binding.

Purpose of the Study:

To develop a graphical user interface (GUI) for interactive exploration of antibody clonal evolution.
To complement existing algorithms like IgPhyML and Dnaml for immunoglobulin lineage reconstruction.
To visualize immunoglobulin phylogenetic trees, mutations, and sequence alignments.

Main Methods:

Utilized the Immcantation framework for adaptive immune receptor sequencing (AIRR-Seq) data analysis.
Employed IgPhyML (from Change-O package) and Phylip for phylogenetic tree construction.
Developed AncesTree, a Java-based GUI for interactive visualization and analysis.

Main Results:

AncesTree provides an interactive platform to explore antibody phylogenetic trees and clonal evolution.
The GUI integrates data from specialized antibody tools for enhanced analysis.
The application is a standalone Java program compatible with Windows, Linux, and Mac OS.

Conclusions:

AncesTree facilitates a deeper understanding of antibody lineage evolution and somatic hypermutation.
The tool enhances the analysis of AIRR-Seq data by providing interactive visualization.
Researchers can now more effectively study the generation of high-affinity antibodies.